Is it possible to make new node connections in .cc file? I mean can I leave the connection part in .ned file empty and define connections in .cc file according to my algorithm?
Sure. Take a look at the manual. It's as easy as:
srcGate->connectTo(destGate);
or a bit more code if you need to use channels:
cGate *outGate, *inGate;
...
// find factory object and create a channel
cChannelType *channelType = cChannelType::get("foo.util.Channel");
cChannel *channel = channelType->create("channel");
// create connecting
outGate->connectTo(inGate, channel);